The use of intra-oral three-dimensional (3D) scanners is becoming increasingly widespread. These scanners produce digital 3D models which represent the 3D structure of a patient's dentition, including both hard and relevant soft tissues. These 3D scans are useful in many applications, most commonly for digital dental and orthodontic workflows such as in the creation of crowns, implants, and appliances. Using these intra-oral scanners, it is possible to acquire 3D scans of both the maxillary and mandibular arches. In general, the digital 3D representations of the arches may not be placed in an orientation with respect to the desired viewpoint or even with respect to one another. Accordingly, a need exists to automatically detect and adjust those orientations of digital 3D dental arch pairs.